ArticleF1000Research2016
Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks.
Article in F1000Research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it, 25 citations in OpenAlex.
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- The Identification of Potential Drugs for Dengue Hemorrhagic Fever: Network-Based Drug Reprofiling Study.JMIR bioinformatics and biotechnology · 2023Article
- Internal control of brain networks via sparse feedback.AIChE journal. American Institute of Chemical Engineers · 2023Article
- Prediction and analysis of osteoarthritis hub genes with bioinformatics.Annals of translational medicine · 2023Article
- Review
- Genome profiles of pathologist-defined cell clusters by multiregional LCM and G&T-seq in one triple-negative breast cancer patient.Cell reports. Medicine · 2021Article
- Zika Virus Infection of Human Iris Pigment Epithelial Cells.Frontiers in immunology · 2021Article
- PD_BiBIM: Biclustering-based biomarker identification in ESCC microarray data.Journal of biosciences · 2021Article
- Hypothetical Proteins as Predecessors of Long Non-coding RNAs.Current genomics · 2020Review
- Oral lichen planus interactome reveals CXCR4 and CXCL12 as candidate therapeutic targets.Scientific reports · 2020Article
- Hypoxic exosomes facilitate angiogenesis and metastasis in esophageal squamous cell carcinoma through altering the phenotype and transcriptome of endothelial cells.Journal of experimental & clinical cancer research : CR · 2019Article
- Bioinformatics analysis of microRNA expression between patients with and without latent tuberculosis infections.Experimental and therapeutic medicine · 2019Article
- Article
- Immunological Molecular Responses of Human Retinal Pigment Epithelial Cells to Infection WithFrontiers in immunology · 2019Article
- Agrin has a pathological role in the progression of oral cancer.British journal of cancer · 2018Article
- Systems Genomics of Thigh Adipose Tissue From Asian Indian Type-2 Diabetics Revealed Distinct Protein Interaction Hubs.Frontiers in genetics · 2018Article
- Bioinformatic analysis of differential expression and core GENEs in breast cancer.International journal of clinical and experimental pathology · 2018Article
- Insights from the protein-protein interaction network analysis of Mycobacterium tuberculosis toxin-antitoxin systems.Bioinformation · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes (e.g. genes or proteins that are differentially expressed) than expected by chance. In a case study, we use CHAT to construct a network of genes that are differentially expressed in Dengue fever, a viral infection. CHAT was used to identify and compare contextual and degree-based hubs in this network. The top 20 degree-based hubs were enriched in pathways related to the cell cycle and cancer, which is likely due to the fact that proteins involved in these processes tend to be highly connected in general. In comparison, the top 20 contextual hubs were enriched in pathways commonly observed in a viral infection including pathways related to the immune response to viral infection. This analysis shows that such AVAILABILITY: CHAT is available for Cytoscape 3.0+ and can be installed via the Cytoscape App Store ( http://apps.cytoscape.org/apps/chat).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.